Journal articles: 'BIOLOG™ EcoPlate'

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Edwar, Suji, and Pingkan Aditiawati. "Analysis of Bacterial Community level Physiological Profiling on the Fermentation of Traditional Pliek u using BIOLOG EcoPlates." 3BIO: Journal of Biological Science, Technology and Management 3, no. 1 (July 13, 2021): 18–27. http://dx.doi.org/10.5614/3bio.2021.3.1.3.

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Pliek u is an Acehnese traditional condiment made from fermented coconut (Cocos nucifera) endosperm. The traditional pliek u fermentation process typically involves a diverse bacterial community. This research aimed to discover the physiological profile of the bacterial community diversity in pliek u fermentation. BIOLOGTM EcoPlates was used to obtain the physiological functions of the bacterial community during the pliek u fermentation process. The bacteria were then isolated from EcoPlate substrate to determine the predominant microorganism. Results from the analysis showed that the value of the Average Well Colour Development (AWCD) increased during the EcoPlates incubation period. The AWCD values in sample IV were higher than the AWCD values in samples I, II, and III. PCA analysis showed that the use of EcoPlate substrate by the bacterial community at the beginning of the fermentation was correlated with the substrate groups of carbohydrate and polymer, and with the substrate groups of carbohydrate and the amino acid at the end of the fermentation. The phylogenetic analysis showed that EC1 had a close relation with Pseudomonas azotoformans strain NBRC, while EC3 had a close relation with Psedomonas lundensis strain ATCC 49968. In conclusion, there were changes in the use of EcoPlate substrate and the activities of the bacterial community during the pliek u fermentation process.

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Koner, Suprokash, Jung-Sheng Chen, Bing-Mu Hsu, Chao-Wen Tan, Cheng-Wei Fan, Tsung-Hsien Chen, Bashir Hussain, and Viji Nagarajan. "Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves." Microorganisms 9, no. 8 (August 23, 2021): 1789. http://dx.doi.org/10.3390/microorganisms9081789.

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Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

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Gajda, Anna M., Ewa A. Czyż, Karolina Furtak, and Krzysztof Jończyk. "Effects of crop production practices on soil characteristics and metabolic diversity of microbial communities under winter wheat." Soil Research 57, no. 2 (2019): 124. http://dx.doi.org/10.1071/sr18113.

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The aim of this research was to compare the effects of organic (ORG, no mineral fertilisers and pesticides) and conventional (CON, with mineral fertilisation and plant protection chemicals) crop production systems on some soil properties: soil organic matter (SOM) and particulate organic matter (POM) contents, dehydrogenase activity and metabolic microbial diversity (Biolog EcoPlate™). Samples of Haplic Luvisol soil were collected from 23-year-old experimental fields under winter wheat from the depth layers of 0–5, 5–10, 15–20 and 30–35cm. Soil under ORG showed higher contents of SOM, POM and POM expressed as a percentage of SOM by 16.0%, 25.6% and 23.9% respectively, in particular down to 5cm depth, compared with the CON system. Also, dehydrogenase activity was 47.5% higher under the ORG than the CON system. The Biolog EcoPlate revealed higher metabolic microbial diversity in soil under ORG crop production system compared with CON. This result was supported by the average well colour development and Shannon’s diversity index values. Significant correlations between soil quality parameters and winter wheat yield confirmed their effectiveness as indicators of soil disturbance. The results showed that the ORG system much better maintained SOM and soil fertility compared with CON.

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Lee, Eun Young, and Sun Hwa Hong. "Assessment of the Changes in the Microbial Community in Alkaline Soils using Biolog Ecoplate and DGGE." KSBB Journal 28, no. 5 (October 30, 2013): 275–81. http://dx.doi.org/10.7841/ksbbj.2013.28.5.275.

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Németh, Imre, Szabina Molnár, Emese Vaszita, and Mónika Molnár. "The Biolog EcoPlate™ Technique for Assessing the Effect of Metal Oxide Nanoparticles on Freshwater Microbial Communities." Nanomaterials 11, no. 7 (July 8, 2021): 1777. http://dx.doi.org/10.3390/nano11071777.

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The application of Biolog EcoPlate™ for community-level physiological profiling of soils is well documented; however, the functional diversity of aquatic bacterial communities has been hardly studied. The objective of this study was to investigate the applicability of the Biolog EcoPlate™ technique and evaluate comparatively the applied endpoints, for the characterisation of the effects of metal oxide nanoparticles (MONPs) on freshwater microbial communities. Microcosm experiments were run to assess the effect of nano ZnO and nano TiO2 in freshwater at 0.8–100 mg/L concentration range. The average well colour development, substrate average well colour development, substrate richness, Shannon index and evenness, Simpson index, McIntosh index and Gini coefficient were determined to quantify the metabolic capabilities and functional diversity. Comprehensive analysis of the experimental data demonstrated that short-term exposure to TiO2 and ZnO NPs affected the metabolic activity at different extent and through different mechanisms of action. TiO2 NPs displayed lower impact on the metabolic profile showing up to 30% inhibition. However, the inhibitory effect of ZnO NPs reached 99% with clearly concentration-dependent responses. This study demonstrated that the McIntosh and Gini coefficients were well applicable and sensitive diversity indices. The parallel use of general metabolic capabilities and functional diversity indices may improve the output information of the ecological studies on microbial communities.

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Gryta, Agata, Magdalena Frąc, and Karolina Oszust. "The Application of the Biolog EcoPlate Approach in Ecotoxicological Evaluation of Dairy Sewage Sludge." Applied Biochemistry and Biotechnology 174, no. 4 (August 14, 2014): 1434–43. http://dx.doi.org/10.1007/s12010-014-1131-8.

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Furtak, Karolina, Jarosław Grządziel, Anna Gałązka, and Jacek Niedźwiecki. "Analysis of Soil Properties, Bacterial Community Composition, and Metabolic Diversity in Fluvisols of a Floodplain Area." Sustainability 11, no. 14 (July 19, 2019): 3929. http://dx.doi.org/10.3390/su11143929.

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The quality of a soil environment affects the microbial community that inhabits it. We decided to examine whether soils formed from river sediments, located in an area of high biodiversity of organisms, are fertile and microbiologically diverse. Fluvisols are considered to be one of the most fertile soils. In this research, bacterial and metabolic diversity, as well as physico–chemical parameters, in three Fluvisols from the Vistula River Gorge of Lesser Poland was investigated. The analysis of physico–chemical and biological parameters demonstrated statistically significant differences between the three Fluvisols examined. While determining the metabolic potential of soil microbiomes with the use of the EcoPlate™ Biolog® technique, we also noted variation between the Fluvisols; however, they were arranged in a significantly different manner from other properties. The next generation sequencing method enabled us to determine the microorganisms common to three Fluvisols, and we identified bacteria specific to individual soils. These results corresponded with the data obtained through EcoPlate™, indicating that the structural diversity and metabolic potential of the microbiome does not always depend on soil quality parameters. Meanwhile, the increased structural diversity of the microbiome was found to improve the metabolic potential of soil microorganisms.

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ASTUTI, DEA INDRIANI, INTAN TAUFIK, DINI ACHNAFANI, and EZRA SUCI PRISCILA. "Physiological Profiling and Microorganism Community Analysis of Cirebon Shrimp Paste Fermentation “Terasi” using BIOLOG TM EcoPlate." Microbiology Indonesia 12, no. 1 (2018): 15–22. http://dx.doi.org/10.5454/mi.12.1.3.

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An, Nan-Hee, Sang-Min Lee, Jung-Rai Cho, Byung-Mo Lee, Jae-Hun Shin, Jung-Hun Ok, and Seok-Cheol Kim. "Effects of Long-Term Fertilization on Microbial Diversity in Upland Soils Estimated by Biolog Ecoplate and DGGE." Korean Journal of Soil Science and Fertilizer 47, no. 6 (December 31, 2014): 451–56. http://dx.doi.org/10.7745/kjssf.2014.47.6.451.

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Sohn, Soo-In, Jae-Hyung Ahn, Subramani Pandian, Young-Ju Oh, Eun-Kyoung Shin, Hyeon-Jung Kang, Woo-Suk Cho, Youn-Sung Cho, and Kong-Sik Shin. "Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties." International Journal of Molecular Sciences 22, no. 11 (May 25, 2021): 5577. http://dx.doi.org/10.3390/ijms22115577.

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Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

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Chávez, Luis Fernando, Luisa Fernanda Escobar, Ibanor Anghinoni, Paulo César de Faccio Carvalho, and Egon José Meurer. "Diversidade metabólica e atividade microbiana no solo em sistema de integração lavoura-pecuária sob intensidades de pastejo." Pesquisa Agropecuária Brasileira 46, no. 10 (October 2011): 1254–61. http://dx.doi.org/10.1590/s0100-204x2011001000020.

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O objetivo deste trabalho foi avaliar a diversidade metabólica e a atividade microbiana, em sistema de integração lavoura-pecuária em plantio direto, sob diferentes intensidades de pastejo e produção de soja. O experimento foi realizado em São Miguel das Missões, RS, em Latossolo Vermelho distroférrico argiloso, submetido ao pastejo a 10, 20, 30 e 40 cm de altura de azevém + aveia-preta, e sem pastejo, no inverno. A diversidade metabólica foi avaliada com microplacas Biolog EcoPlate pelo índice de diversidade de Shannon, e a atividade microbiana pelo método de hidrólise do diacetato de fluoresceína. Houve maior diversidade funcional a intensidades moderadas de pastejo (20 a 40 cm). A maior atividade microbiológica no solo ocorreu no tratamento sem pastejo, em consequência da grande quantidade de resíduos vegetais remanescentes. A diversidade funcional da microbiota e a atividade microbiana tiveram alterações causadas pelas intensidades de pastejo, que podem ser utilizadas como indicadores de qualidade do solo, em sistema de integração lavoura-pecuária em plantio direto.

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Furtak, Karolina, Jarosław Grządziel, and Anna Gałązka. "Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event." Biology 11, no. 3 (March 1, 2022): 386. http://dx.doi.org/10.3390/biology11030386.

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Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned.

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Karolina, Furtak, Gawryjołek Karolina, Gajda Anna M, and Gałązka Anna. "Effects of maize and winter wheat grown under different cultivation techniques on biological activity of soil." Plant, Soil and Environment 63, No. 10 (November 2, 2017): 449–54. http://dx.doi.org/10.17221/486/2017-pse.

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The aim of the study was to compare the activity and functional biodiversity in soil under two different cereals: common maize and winter wheat, both grown in the same pattern of cultivation techniques: conventional (to 25 cm depth) and reduced (to 10 cm depth). Soil samples for comparative analysis were collected at the same time (July 2016) at a long-term field experiment, which was carried out in 2013–2016. Soil biological activity was determined by measurement of dehydrogenases activity (DHa) with TTC (2,3,5-triphenyltetrazolium chloride) application, microbial biomass carbon (MBC) and nitrogen (MBN) content by fumigation-extraction method, and functional diversity of soil microorganisms using the Biolog EcoPlate System. The results demonstrated that the cultivation technique had a greater impact on the soil biological activity, compared to the type of cereal. Higher biological activity was found in the soil under reduced tillage in both cereals. Calculated correlations showed that DHa, MBC, MBN and acid phosphatases were positively correlated with each other. The negative correlation obtained between yield and biological parameters of activity in soil was not expected.

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Candan, Esra Deniz, Neslihan İdil, and Onur Candan. "The microbial community in a green turtle nesting beach in the Mediterranean: application of the Biolog EcoPlate approach for beach pollution." Environmental Science and Pollution Research 28, no. 36 (May 3, 2021): 49685–96. http://dx.doi.org/10.1007/s11356-021-14196-8.

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Grządziel, Jarosław, Karolina Furtak, and Anna Gałązka. "Community-Level Physiological Profiles of Microorganisms from Different Types of Soil That are Characteristic to Poland—a Long-Term Microplot Experiment." Sustainability 11, no. 1 (December 21, 2018): 56. http://dx.doi.org/10.3390/su11010056.

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Comparative studies, such as the analysis of physicochemical properties and the microbiological composition of soil, are burdened with many problems resulting from the various locations of soils—often, different weather conditions among the experimental fields and varying time between the sample collection and analysis. The aim of this study was to assess the differences in the physiological profiles of bacterial communities from eight different types of soils from Poland, used in the microplot experiment that was established in 1881. The same plant species were continuously grown at all plots, at the same time, and the soil received the same type of fertilization. Moreover, the soils were always under the same weather conditions. The community-level physiological profiles of microorganisms were evaluated by using the Biolog EcoPlate™ method. The analysis demonstrated that good quality soils, especially the Gleyic Chernozem, Cambic Leptosol, and the Fluvic Cambisol exhibit a significantly higher enzyme activity, compared with the dystric soils. The dehydrogenases activity in the different time-points indicates a wide soil microbiome buffering capacity, which allows the persistence of a relatively permanent physiological profile, over many years.

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Wolińska, Agnieszka, Anna Gałązka, Agnieszka Kuźniar, Weronika Goraj, Natalia Jastrzębska, Jarosław Grządziel, and Zofia Stępniewska. "Catabolic Fingerprinting and Diversity of Bacteria in Mollic Gleysol Contaminated with Petroleum Substances." Applied Sciences 8, no. 10 (October 18, 2018): 1970. http://dx.doi.org/10.3390/app8101970.

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This study focused on the determination of both catabolic and genetic fingerprinting of bacteria inhabiting soil contaminated with car fuels. A surface layer (0–20 cm) of Mollic Gleysol was used for the experiment and was contaminated with car fuels—unleaded 95-octane petrol and diesel at a dose of 15 g per 10 g of soil. The experiment lasted 42 days and was performed at 20 °C. The metabolic potential of soil bacterial communities was evaluated using the Biolog EcoPlate system. The results demonstrated that petroleum substances influenced the structure of the microbial populations and their catabolic activity. The Arthrobacter, Paenibacillus, and Pseudomonas genera were found in diesel-contaminated soil, whilst Bacillus and Microbacterium were found in petrol-contaminated soil. Rhodococcus species were identified in both variants of impurities, suggesting the widest capability of car fuel degradation by this bacterial genus. The contamination with unleaded 95-octane petrol caused rapid inhibition of the metabolic activity of soil bacteria in contrast to the diesel treatment, where high metabolic activity of bacteria was observed until the end of the incubation period. Higher toxicity of petrol in comparison with diesel car fuel was evidenced.

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Wang, G., J. Jin, X. Chen, J. Liu, X. Liu, and S. J. Herbert. "Biomass and catabolic diversity of microbial communities with long-term restoration, bare fallow and cropping history in Chinese Mollisols." Plant, Soil and Environment 53, No. 4 (January 7, 2008): 177–85. http://dx.doi.org/10.17221/2313-pse.

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Microbial biomass and community catabolic diversities at three depths (0−10 cm, 20−30 cm, and 40−50 cm) in Chinese Mollisols as influenced by long-term managements of natural restoration, cropping and bare fallow were investigated. Microbial biomass was estimated from chloroform fumigation-extraction and substrate-induced respiration (SIR), and catabolic diversity was determined by using Biolog® EcoPlate. Experimental results showed that microbial biomass significantly declined with soil depth in the treatments of restoration and cropping, and not in the treatment of bare fallow, where the microbial biomass had a positive relationship with the total soil C content. The inspections into the catabolic capability of the microbial community at the same soil depth showed that the treatment of natural restoration had a relatively stronger metabolic ability than the cropping and bare fallow treatments. Shannon”s diversity index, substrate richness and substrate evenness calculated from the Biolog data were higher in the treatments of natural restoration and cropping than the bare fallow treatment with the same soil depth, and with the highest values in the top soil. Principal component analysis indicated that the catabolic profiles not only varied with the soil depth in each treatment, but also differed in the three treatments within the same soil depth. The catabolic profiles of the three treatments were similar to each other in the soil depth of 0−10 cm and distinctly different in the soil depths of 20−30 cm and 40−50 cm. These results suggest that it was microbial biomass rather than community function that was influenced by the different soil management in the topsoil (0−10 cm); in the relative depths, the soil microbial community function was more easily influenced than microbial biomass.

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Lan, Xiu, Hu Du, Wanxia Peng, Yongxian Liu, Zhilian Fang, and Tongqing Song. "Functional Diversity of the Soil Culturable Microbial Community in Eucalyptus Plantations of Different Ages in Guangxi, South China." Forests 10, no. 12 (November 28, 2019): 1083. http://dx.doi.org/10.3390/f10121083.

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We selected five different ages of eucalyptus plantation sites to understand the culturable microbial functional diversity and the ecological functions of the soil from the eucalyptus plantations in Guangxi. We investigated the carbon source metabolic activity and diversity features of surface soil microbes using the Biolog EcoPlate method (Biolog Inc., Hayward, CA, USA), along with the microbial functional diversity and physicochemical properties of the soil. The results suggest that the carbon source utilization capacity of the soil microbes at various forest ages manifested as 3-year-old > 5-year-old > 2-year-old > 1-year-old > 8-year-old. The abundance, Shannon–Weiner, Pielou, Simpson, and McIntosh diversity indices of the soil microbes initially increased and then decreased with further increase in forest age, with the highest levels in 3- and 5-year-old forests. As per the heatmap analysis, the 3-year-old forest could metabolize the most carbon source species, while the 1- and 8-year-old forests could metabolize the least. Carbohydrates were the most frequently metabolized carbon source. The principal component analysis (PCA) shows that PC1 and PC2 extracted from the 31 factors have 52.42% and 13.39% of the variable variance, respectively. Carbohydrates contributed most to PCA, followed by amino acids and carboxylic acids, and phenolic acids and amines, the least. Canonical correspondence analysis shows that total carbon, alkali-hydrolyzable nitrogen, total nitrogen, total potassium, and pH negatively correlate with soil microbial functional diversity, whereas total and available phosphorus positively correlate with it. To sum up, the soil microbial community structure of eucalyptus plantations at various ages reflects the soil environmental conditions and nutrient availability, which is of great significance in the efficient management and high-quality operation of their plantations in Guangxi.

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Cacchio, Paola, and Maddalena Del Gallo. "A Novel Approach to Isolation and Screening of Calcifying Bacteria for Biotechnological Applications." Geosciences 9, no. 11 (November 14, 2019): 479. http://dx.doi.org/10.3390/geosciences9110479.

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Bacterial calcium-carbonate precipitation (BCP) has been studied for multiple applications such as remediation, consolidation, and cementation. Isolation and screening of strong calcifying bacteria is the main task of BCP-technique. In this paper, we studied CaCO3 precipitation by different bacteria isolated from a rhizospheric soil in both solid and liquid media. It has been found, through culture-depending studies, that bacteria belonging to Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria are the dominant bacteria involved in CaCO3 precipitation in this environment. Pure and mixed cultures of selected strains were applied for sand biocementation experiments. Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) analyses of the biotreated samples revealed the biological nature of the cementation and the effectiveness of the biodeposition treatment by mixed cultures. X-ray diffraction (XRD) analysis confirmed that all the calcifying strains selected for sand biocementation precipitated CaCO3, mostly in the form of calcite. In this study, Biolog® EcoPlate is evaluated as a useful method for a more targeted choice of the sampling site with the purpose of obtaining interesting candidates for BCP applications. Furthermore, ImageJ software was investigated, for the first time to our knowledge, as a potential method to screen high CaCO3 producer strains.

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Anna M, Gajda, Czyż Ewa A, Stanek-Tarkowska Jadwiga, Dexter Anthony R, Furtak Karolina M, and Grządziel Jarosław. "Effects of long-term tillage practices on the quality of soil under winter wheat." Plant, Soil and Environment 63, No. 5 (May 17, 2017): 236–42. http://dx.doi.org/10.17221/223/2017-pse.

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These studies were done in 2013–2016 on the effects of two tillage systems on the quality of a loamy sand soil (Eutric Fluvisol) and were based on a field experiment started in 2002. Winter wheat was grown in conventional tillage (CT) with mouldboard ploughing (inversion) tillage; and reduced (non-inversion) tillage (RT) based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as mulch in both treatments. The physical, chemical and biological properties of the soil were investigated. RT increased soil bulk density in the 0–5 cm and 5–10 cm depth layers in comparison with CT. The greatest content of soil organic carbon (SOC) was found in the 0–5 cm layer under RT. The BIOLOG EcoPlate System showed that soil under RT had a greater metabolic activity and diversity of microbial communities than soil under CT. RT improved the quality of the surface soil as shown by the greater content of SOC and microbial activity measured in terms of dehydrogenases. However, the mean yields of winter wheat under RT and CT were similar. This suggests that the effects of increased bulk density (BD) on yield can be compensated by the effects of the improved microbial status.

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Xue, Qi, Yang Xiang, Xiao-Qin Wu, and Ming-Jie Li. "Bacterial Communities and Virulence Associated with Pine Wood Nematode Bursaphelenchus xylophilus from Different Pinus spp." International Journal of Molecular Sciences 20, no. 13 (July 7, 2019): 3342. http://dx.doi.org/10.3390/ijms20133342.

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Bursaphelenchus xylophilus, the causal agent of pine wilt disease, is a destructive threat to pine forests. The role of bacteria associated with B. xylophilus in pine wilt disease has attracted widespread attention. This study investigated variation in bacterial communities and the virulence of surface-sterilized B. xylophilus from different Pinus spp. The predominant culturable bacteria of nematodes from different pines were Stenotrophomonas and Pseudomonas. Biolog EcoPlate analysis showed that metabolic diversity of bacteria in B. xylophilus from P. massoniana was the highest, followed by P. thunbergii and P. densiflora. High-throughput sequencing analysis indicated that bacterial diversity and community structure in nematodes from the different pine species varied, and the dominant bacteria were Stenotrophomonas and Elizabethkingia. The virulence determination of B. xylophilus showed that the nematodes from P. massoniana had the greatest virulence, followed by the nematodes from P. thunbergii and P. densiflora. After the nematodes were inoculated onto P. thunbergii, the relative abundance of the predominant bacteria changed greatly, and some new bacterial species emerged. Meanwhile, the virulence of all the nematode isolates increased after passage through P. thunbergii. These inferred that some bacteria associated with B. xylophilus isolated from different pine species might be helpful to adjust the PWN’s parasitic adaptability.

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Feigl, Viktória, Éva Ujaczki, Emese Vaszita, and Mónika Molnár. "Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies." Science of The Total Environment 595 (October 2017): 903–11. http://dx.doi.org/10.1016/j.scitotenv.2017.03.266.

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King, Gary M. "Contributions of Atmospheric CO and Hydrogen Uptake to Microbial Dynamics on Recent Hawaiian Volcanic Deposits." Applied and Environmental Microbiology 69, no. 7 (July 2003): 4067–75. http://dx.doi.org/10.1128/aem.69.7.4067-4075.2003.

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ABSTRACT A series of sites were established on Hawaiian volcanic deposits ranging from about 18 to 300 years old. Three sites occurred in areas that supported tropical rain forests; the remaining sites were in areas that supported little or no plant growth. Sites >26 years old consumed atmospheric CO and hydrogen at rates ranging from about 0.2 to 5 mg of CO m−2 day−1 and 0.1 to 4 mg of H2 m−2 day−1, respectively. Respiration, measured as CO2 production, for a subset of the sites ranged from about 40 to >1,400 mg of CO2 m−2 day−1. CO and H2 accounted for about 13 to 25% of reducing equivalent flow for all but a forested site, where neither substrate appeared significant. Based on responses to chloroform fumigation, hydrogen utilization appeared largely due to microbial uptake. In contrast to results for CO and hydrogen, methane uptake occurred consistently only at the forest site. Increasing deposit age was generally accompanied by increasing concentrations of organic matter and microbial biomass, measured as phospholipid phosphate. Exoenzymatic activities (acid and alkaline phosphatases and α- and β-glucosidases) were positively correlated with deposit age in spite of considerable variability within sites. The diversity of substrates utilized in Biolog Ecoplate assays also increased with deposit age, possibly reflecting changes in microbial community complexity.

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Siebielec, Sylwia, Grzegorz Siebielec, Piotr Sugier, Małgorzata Woźniak, Jarosław Grządziel, Anna Gałązka, and Tomasz Stuczyński. "Activity and Diversity of Microorganisms in Root Zone of Plant Species Spontaneously Inhabiting Smelter Waste Piles." Molecules 25, no. 23 (November 30, 2020): 5638. http://dx.doi.org/10.3390/molecules25235638.

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The aim was to assess plant driven changes in the activity and diversity of microorganisms in the top layer of the zinc and lead smelter waste piles. The study sites comprised two types (flotation waste—FW and slag waste—SW) of smelter waste deposits in Piekary Slaskie, Poland. Cadmium, zinc, lead, and arsenic contents in these technosols were extremely high. The root zone of 8 spontaneous plant species (FW—Thymus serpyllum, Silene vulgaris, Solidago virgaurea, Echium vulgare, and Rumex acetosa; and SW—Verbascum thapsus; Solidago gigantea, Eupatorium cannabinum) and barren areas of each waste deposit were sampled. We observed a significant difference in microbial characteristics attributed to different plant species. The enzymatic activity was mostly driven by plant-microbial interactions and it was significantly greater in soil affected by plants than in bulk soil. Furthermore, as it was revealed by BIOLOG Ecoplate analysis, microorganisms inhabiting barren areas of the waste piles rely on significantly different sources of carbon than those found in the zone affected by spontaneous plants. Among phyla, Actinobacteriota were the most abundant, contributing to at least 25% of the total abundance. Bacteria belonging to Blastococcus genera were the most abundant with the substantial contribution of Nocardioides and Pseudonocardia, especially in the root zone. The contribution of unclassified bacteria was high—up to 38% of the total abundance. This demonstrates the unique character of bacterial communities in the smelter waste.

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Silveira, Géssica Aparecida, Luciana Maria Saran, Wanderley José de Melo, and Lucia Maria Carareto Alves. "Farming and soil urban occupation in the water quality of Jaboticabal and Cerradinho streams." Ciência e Agrotecnologia 40, no. 6 (December 2016): 633–46. http://dx.doi.org/10.1590/1413-70542016406048415.

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ABSTRACT Since the end of the twentieth century, 100% of the urban sewage from the city of Jaboticabal has been collected by interceptors and routed to a treatment plant. Between 1999 and 2000, studies on the effect of this environmental care showed that it did not efficiently clean up the water from the two streams that run through the city and flow into an agricultural area. This paper focuses on assessing the influence of soil use on the water quality of surface waters from these two streams. The study was conducted 15 years after the implementation of sewage interceptors. The sampling dates were bimonthly at eight points (P1 to P8) in the Cerradinho and Jaboticabal streams, in Jaboticabal (São Paulo State, Brazil). P1 was located at the source of the Jaboticabal stream, P2 was in a farming area, P3, P4 and P5 were in an urban area, and P6, P7 and P8 were in a farming area. The physical and chemical variables of the water were assessed. We compared the ability of microorganisms to metabolize different sources of carbon using the EcoPlate (Biolog). The total phosphorus (TP) concentration exceeded the limit set by the Brazilian legislation as well as values found in previous studies, which was also observed for the chemical oxygen demand. However, the bacterial metabolic profile had no association with urban or farming practices. The results of the analysis indicated the possibility of clandestine discharge of wastewater in the streams studied and the influence of the agricultural soil.

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Nguyen Quoc, Tuan, Zahra Derakhshan Nejad, and Myung Chae Jung. "Effect of Commercial Amendments on Immobilization of Arsenic, Copper, and Zinc in Contaminated Soil: Comprehensive Assessing to Plant Uptake Combined with a Microbial Community Approach." Minerals 11, no. 10 (October 18, 2021): 1143. http://dx.doi.org/10.3390/min11101143.

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Identifying the proper chemical and biological materials as soil amendments is a great concern because they replace soil properties and subsequently change the soil quality. Hence, this study was conducted to evaluate the effects of a diverse range of soil amendments including bentonite (B), talc (T), activated carbon (AC), and cornstarch (CS) in form of sole and composite on the immobilization and bioavailability of As, Cu, and Zn. The amendments were characterized by SEM, FT-IR, and XRF, and applied at 2% (w/w) in the experimental pots with an Asteraceae (i.e., lettuce) for 45 days to monitor plant growth parameters and soil microbial community. Soil pH from 6.1 ± 0.02 significantly increased in the amended soils with the maximum value found for TAC (7.4 ± 0.04). The results showed that soil amendments reduced easily in an exchangeable fractionation of As, Cu, and Zn with the maximum values found for BAC by 66.4%, AC by 84.2%, and T by 89.7% respectively. Adding B, T, AC, and their composites induced dry biomass of lettuce >40 wt.%, while CS and its composites did not affect the dry biomass of the plant. The average content of Cu and Zn in plant tissues decreased >45 wt.% in B, AC, and their composites amended soils; meanwhile, AC and its composites mitigated As uptake by >30 wt.% in lettuce. The results of Biolog Ecoplate showed that the amending soils improved the microbial community, especially for composites (e.g., TCS). The results demonstrated that adding composites amendments provided an efficient method for the immobilization of metals and metalloids, and also induced plant growth parameters and microbial community.

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Almendras, Katerin, Diego Leiva, Margarita Carú, and Julieta Orlando. "Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest." Molecules 23, no. 11 (October 24, 2018): 2746. http://dx.doi.org/10.3390/molecules23112746.

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Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.

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Wei, Zongqiang, Shaohua Wu, Shenglu Zhou, and Chen Lin. "Installation of impervious surface in urban areas affects microbial biomass, activity (potential C mineralisation), and functional diversity of the fine earth." Soil Research 51, no. 1 (2013): 59. http://dx.doi.org/10.1071/sr12089.

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Artificial soil sealing in urban areas has attracted increasing attention due to its potential hazard to urban ecosystems. It has negative impacts on soil function and the urban environment, since the impervious surface can hamper the exchange of material and energy between the soil and other environmental compartments. However, information about the effects of artificial soil sealing in urban area on soil quality and properties, especially the microbiological components, is still limited. Ten plots which differed in land use were selected from Nanjing City, China, to investigate the effects of impervious surfaces on microbiological characteristics in urban soil. Plot types were paved road, residential paved square, residential paved alley, and grassed area. Soil microbial biomass carbon (Cmic) and nitrogen (Nmic), and activities were analysed, and the microbial functional diversity of fine earth (<2 mm material) was characterised by the Biolog EcoPlate technique. Mean concentrations of soil organic carbon (SOC), Cmic, and Nmic in fine earth from the impervious areas (0–20 cm) were, respectively, 6.5 g kg–1, 55.8 mg kg–1, and 12.2 mg kg–1, which were significantly lower than concentrations from grass areas. Urban sealing also resulted in decreases in soil microbial activity and functional diversity, but the influences on soil microbial diversity varied among land uses, with road pavement having the most negative effect. Substrate use patterns showed that microorganisms in urban sealed soils had higher utilisation of polymers (P < 0.05) but lower use of carbohydrates and amines/amides (P < 0.05). These findings demonstrate that SOC in the sealed soils was more stable than in open soils, and the installation of impervious surfaces such as asphalt and concrete, which are very common in urban areas, can result in decreases in SOC content, soil microbial activity, and diversity in urban soil.

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Ferreira, M., C. Reinhardt, M. Rijst, A. Marais, and A. Botha. "Allelopathic Root Leachate Effects of Lolium multiflorum x L. perenne on Crops and the Concomitant Changes in Metabolic Potential of the Soil Microbial Community as Indicated by the Biolog Ecoplate™." International Journal of Plant & Soil Science 19, no. 5 (January 10, 2017): 1–14. http://dx.doi.org/10.9734/ijpss/2017/36918.

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Reynolds-Clausen, Kelley, Karen Surridge-Talbot, Marelize Botes, and T. Eugene Cloete. "Bacterial species diversity as an indicator of dibromonitrilopropionamide (DBNPA) biocide efficacy." Water Science and Technology 78, no. 2 (July 6, 2018): 320–28. http://dx.doi.org/10.2166/wst.2018.289.

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Abstract Microorganism growth in industrial systems is controlled through the use of biocides and biodispersants. There is, however, no simple means of determining the efficacy of these control mechanisms, but it is currently tested using complex bacterial culturing techniques. Biolog Ecoplates® have been used to detect bacterial population changes in various communities. These microtitre plates comprise 31 different carbon substrates (in triplicate) with wells. When a sample is added to the wells, bacteria capable of metabolising the relevant carbon sources respire the substrates, causing the tetrazolium dye in the well to turn purple, indicating a positive result. Hypothetically, the higher the microbial diversity, the more substrates will be utilised and vice versa. The objective of this study was to test this hypothesis, using Biolog Ecoplates® as a potential simple indicator to determine the efficiency of a biocide to control microbial growth in cooling water systems by monitoring the changes in the microbial metabolic pattern. This study proved the hypothesis using Biolog Ecoplates®, indicating that the addition of biocides at various concentrations resulted in fewer substrates being utilised, indicative of a decrease in microbial species diversity.

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Sofo, Adriano, and Patrizia Ricciuti. "A Standardized Method for Estimating the Functional Diversity of Soil Bacterial Community by Biolog® EcoPlatesTM Assay—The Case Study of a Sustainable Olive Orchard." Applied Sciences 9, no. 19 (September 26, 2019): 4035. http://dx.doi.org/10.3390/app9194035.

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Biolog® EcoPlates™ (Biolog Inc., Hayward, CA, USA) were developed to analyse the functional diversity of bacterial communities by means of measuring their ability to oxidize carbon substrates. This technique has been successfully adopted for studying bacterial soil communities from different soil environments, polluted soils and soils subjected to various agronomic treatments. Unfortunately, Biolog® EcoPlates™ assay, especially working on soil, can be difficult to reproduce and hard to standardize due to the lack of detailed procedures and protocols. The main problems of this technique mainly regard soil preparation, bacterial inoculum densities and a correct definition of blank during the calculation of the diversity indices. On the basis of our previous research on agricultural soils, we here propose a standardized and accurate step-by-step method for estimating the functional diversity of a soil bacterial community by Biolog® EcoPlatesTM assay. A case study of soils sampled in a Mediterranean olive orchard managed accordingly to sustainable/conservation practices was reported for justifying the standardized method here used. The results of this methodological paper could be important for correctly evaluating and comparing the microbiological fertility of soils managed by sustainable/conservation or conventional/non-conservation systems.

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Zhao, Qiong, Ke Zhou, Fengfeng Zhang, Yujie Zhao, Haibo Sun, and Fengxing Xie. "Effect of aquaculture water eutrophication on color development in Biolog EcoPlates." Aquaculture International 29, no. 1 (January 9, 2021): 373–86. http://dx.doi.org/10.1007/s10499-020-00632-y.

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Honey, Whitney, Tracey Yenilaitus, and Jeanne Kagle. "Analysis of the Impact of Acid Mine Drainage on Bacterial Populations in the Upper Tioga Watershed." Journal of the Pennsylvania Academy of Science 87, no. 1 (June 1, 2013): 34–41. http://dx.doi.org/10.5325/jpennacadscie.87.1.0034.

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ABSTRACT The Upper Tioga Watershed (UTW) in northern Pennsylvania is exposed to acid mine drainage (AMD), resulting in decreased population sizes and diversity of macrobiota. Few studies thus far, however, have assessed the impact of AMD on the microbial communities in streams receiving AMD. Using taxonomic (terminal restriction fragment length polymorphisms (T-RFLP)) and metabolic (Biolog EcoPlates) analyses, bacterial biodiversity and community structure in AMD-impacted and non-impacted sites of the UTW were compared. The results indicate that bacterial communities in sediments of streams receiving AMD differ from those at a non-impacted site and are less diverse. Analysis of T-RFLP patterns and metabolic patterns from Biolog EcoPlates revealed two main clusters of community similarity among the sites. The pattern suggests that the bacterial communities may be more resistant to negative effects of AMD than macroscopic organisms. One AMD-impacted site is dominated by one taxonomic group, putatively identified as Beijerinckiaceae.

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Tangapo, Agustina. "Potensi Metabolik Komunitas Bakteri Endofit dan Rhizosfer Ubi Jalar (Ipomoea batatas L.) Berdasarkan Analisis Community-Level Physiological Profiles (CLPP)." Jurnal MIPA 9, no. 1 (January 13, 2020): 18. http://dx.doi.org/10.35799/jmuo.9.1.2020.27159.

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Aktivitas metabolik dari komunitas bakteri endofit dan rizosfir diukur untuk membandingkan tingkat community-level physiological profiling (CLPP) menggunakan Biolog Ecoplates. Hasil penelitian kami menunjukkan kepadatan bakteri meningkat dengan urutan: endofit<rhizosfer. Keragaman mikroba dinilai oleh kekayaan spesies, jumlah spesies dan indeks kesamaan. Aktivitas total mikroba tertinggi diamati pada mikroba rhizosfer. CLPP menunjukkan bahwa bakteri bisa memanfaatkan semua kelompok sumber karbon sebagai berikut karbohidrat, asam amino, asam karboksilat, polimer, amina/amida, dan senyawa fenolik. Karbohidrat yang paling dimanfaatkan. Total metabolic activity of endophytic and rhizosphere of bacterial community of sweet potato was measured to compare the community-level physiological profiles (CLPP) using by Biolog Ecoplates. Result of our study revealed that bacterial density increased in the following order: endophytes < rhizosphere. The microbial diversity assessed by species richness, the total number of species present and species evenness. The highest total microbial activity was observed for the rhizosphere. The CLPP revealed that the bacteria could differentially utilize all the groups of carbon sources as follows carbohydrate, amino acid, carboxilyc acid, polymer, amine/amide, and phenolic compound. Carbohydrate was most utilized.

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Xu, Wenhuan, Zhiwei Ge, and Daya Ram Poudel. "Application and Optimization of Biolog EcoPlates in Functional Diversity Studies of Soil Microbial Communities." MATEC Web of Conferences 22 (2015): 04015. http://dx.doi.org/10.1051/matecconf/20152204015.

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Brandstaetter, Christian, Nora Fricko, Mohammad J. Rahimi, Johann Fellner, Wolfgang Ecker-Lala, and Irina S. Druzhinina. "The microbial metabolic activity on carbohydrates and polymers impact the biodegradability of landfilled solid waste." Biodegradation 33, no. 1 (November 23, 2021): 71–85. http://dx.doi.org/10.1007/s10532-021-09967-6.

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AbstractBiological waste degradation is the main driving factor for landfill emissions. In a 2-year laboratory experiment simulating different landfill in-situ aeration scenarios, the microbial degradation of solid waste under different oxygen conditions (treatments) was investigated. Nine landfill simulation reactors were operated in triplicates under three distinct treatments. Three were kept anaerobic, three were aerated for 706 days after an initial anaerobic phase and three were aerated for 244 days in between two anaerobic phases. In total, 36 solid and 36 leachate samples were taken. Biolog® EcoPlates™ were used to assess the functional diversity of the microbial community. It was possible to directly relate the functional diversity to the biodegradability of MSW (municipal solid waste), measured as RI4 (respiration index after 4 days). The differences between the treatments in RI4 as well as in carbon and polymer degradation potential were small. Initially, a RI4 of about 6.5 to 8 mg O2 kg−1 DW was reduced to less than 1 mg O2 kg−1 DW within 114 days of treatment. After the termination of aeration, an increase 3 mg O2 kg−1 DW was observed. By calculating the integral of the Gompertz equation based on spline interpolation of the Biolog® EcoPlates™ results after 96 h two substrate groups mainly contributing to the biodegradability were identified: carbohydrates and polymers. The microbial activity of the respective microbial consortium could thus be related to the biodegradability with a multilinear regression model.

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Checcucci, A., D. Luise, M. Modesto, F. Correa, P. Bosi, P. Mattarelli, and Paolo Trevisi. "Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota." Applied Microbiology and Biotechnology 105, no. 14-15 (July 23, 2021): 6033–45. http://dx.doi.org/10.1007/s00253-021-11449-x.

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Abstract In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology. Key points • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the BiologTMEcoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample. Graphical abstract

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Floch, Carine, Anne-Céline Chevremont, Karine Joanico, Yvan Capowiez, and Stéven Criquet. "Indicators of pesticide contamination: Soil enzyme compared to functional diversity of bacterial communities via Biolog® Ecoplates." European Journal of Soil Biology 47, no. 4 (July 2011): 256–63. http://dx.doi.org/10.1016/j.ejsobi.2011.05.007.

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Zhen Teng, Wei Fan, Huiling Wang, Xiaoqing Cao, and Xiaoniu Xu. "Monitoring Soil Microorganisms with Community-Level Physiological Profiles Using Biolog EcoPlates™ in Chaohu Lakeside Wetland, East China." Eurasian Soil Science 53, no. 8 (August 2020): 1142–53. http://dx.doi.org/10.1134/s1064229320080141.

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Zhao, Qiong, Fengxing Xie, Fengfeng Zhang, Ke Zhou, Haibo Sun, Yujie Zhao, and Qian Yang. "Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2." Aquaculture 546 (January 2022): 737288. http://dx.doi.org/10.1016/j.aquaculture.2021.737288.

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Patel, M., D. R. Tipre, and Shailesh R. Dave. "Microbial Diversity by Substrate Utilization Profiles of Lignite Mines Samples of Gujarat, India." Advanced Materials Research 71-73 (May 2009): 101–4. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.101.

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Microbial diversity studies of lignite mines of Rajpardi, Amod, Tadkeshwar and Panandhro, Gujarat, India, were carried out by substrate utilization-based, community-structure analysis. In Biologâ EcoPlates out of 31 different substrates, 1 to 28 substrates were metabolized. On the basis of these, similarity index and diversity indices were studied. From an extreme mine site Gram-positive, Gram-negative, fungi and yeasts were isolated and identified. One of the yeasts isolated is for the first time reported from a lignite mine ecosystem Apart from this auto- and heterotrophic iron oxidizers; sulphur oxidizers and sulphate reducers were also isolated. So, lignite mine ecosystems, inspite of the extreme environment showed rich microbial diversity.

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Liu, Bei, Yanxia Li, Xuelian Zhang, Jing Wang, and Min Gao. "Effects of chlortetracycline on soil microbial communities: Comparisons of enzyme activities to the functional diversity via Biolog EcoPlates™." European Journal of Soil Biology 68 (May 2015): 69–76. http://dx.doi.org/10.1016/j.ejsobi.2015.01.002.

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Sanchez, Christopher D., J. Benjamin Brown, Omree Gal-Oz, and Esther Singer. "EcoPLOT: dynamic analysis of biogeochemical data." Bioinformatics 38, no. 5 (December 20, 2021): 1480–82. http://dx.doi.org/10.1093/bioinformatics/btab842.

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Abstract Motivation We have created EcoPLOT (parameterized linkage of omics-driven technologies), a web-app for the dynamic, interactive analysis of biogeochemical datasets that combines state-of-the-art analysis tools to statistically and graphically explore environmental, geochemical and microbiome datasets. Using the iterative random forest, a machine learning algorithm, EcoPLOT allows for the de novo discovery of drivers which exhibit significant impact on plant, microbial or soil dynamics. Availability and implementation EcoPLOT is built entirely within the R language. It can be accessed through any system where R is installed, including Windows, Mac and most Linux systems. EcoPLOT is free to use and can be accessed at https://github.com/cdsanchez18/EcoPLOT.

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Anna, Gałązka, Gawryjołek Karolina, Grządziel Jarosław, Frąc Magdalena, and Księżak Jerzy. "Microbial community diversity and the interaction of soil under maize growth in different cultivation techniques." Plant, Soil and Environment 63, No. 6 (June 14, 2017): 264–70. http://dx.doi.org/10.17221/171/2017-pse.

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Soil microbial functional diversity under maize grown in different agricultural management practices was determined using the Biolog EcoPlates and other microbial and biochemical methods. Comparisons of substrate utilization and the diversity indices showed differences in community composition of microorganisms related to different cultivation techniques and seasons. The soil samples collected in spring were characterized by statistically significant lower indices of biological activity in comparison to the soil collected from the flowering stage of maize. The soils collected in spring from the plots with full tillage had a similarly high biological activity as the soils obtained from maize flowering season. The principal component of PC analysis, showed the strong correlation between the parameters of soil quality and biodiversity indicators. Selected indicators of soil microbial diversity explained 71.51% of biological variability in soils. Based on the PC analysis, two major groups of soils have been indicated. Management practices and seasons were two important factors affecting soil microbial communities.

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Urakawa, Hidetoshi, Jaffar Ali, Rheannon D. J. Ketover, Spencer D. Talmage, Juan C. Garcia, Ian S. Campbell, Ai Ning Loh, and Michael L. Parsons. "Shifts of Bacterioplankton Metabolic Profiles along the Salinity Gradient in a Subtropical Estuary." ISRN Oceanography 2013 (December 12, 2013): 1–12. http://dx.doi.org/10.5402/2013/410814.

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Understanding the biodegradation potential of river bacterioplankton communities is crucial for watershed management. We investigated the shifts in bacterioplankton metabolic profiles along the salinity gradient of the Caloosahatchee River Estuary, Florida. The carbon source utilization patterns of river bacterioplankton communities were determined by using Biolog EcoPlates. The number of utilized substrates was generally high in the upstream freshwater dominated zone and low in the downstream zone, suggesting a shift in metabolic profiles among bacterioplankton assemblages along the estuarine gradient. The prokaryotic cell numbers also decreased along the estuarine salinity gradient. Seasonal and site-specific differences were found in the numbers of utilized substrates, which were similar in summer and fall (wet season) and winter and spring (dry season). Bacterioplankton assemblages in summer and fall showed more versatile substrate utilization patterns than those of winter and spring communities. Therefore, our data suggest that microbial metabolic patterns in the subtropical estuary are likely influenced by the water discharge patterns created by dry and wet seasons along the salinity gradient.

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WingChing-Jones, Rodolfo, and Lidieth Uribe Lorío. "Biomass and activity soil microorganisms in grazing and secondary forests areasA." UNED Research Journal 8, no. 1 (June 10, 2016): 107–13. http://dx.doi.org/10.22458/urj.v8i1.1231.

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Sustainable livestock production generates benefits for the environment, such as water capture, increased biodiversity and carbon dioxide capture. To measure these factors in a tropical setting, in 2007 we took three samples of a milk production system in Turrialba, Cartago, Costa Rica, in areas with permanent African Star grass cover (under grazing) and a secondary forest with 15 years of regeneration. We estimated carbon content in the microbial biomass, microbial activity (breathing technique), carbon usage profile (BIOLOG ECOPLATES®) and functional diversity of microorganisms (Shannon index). Biomass carbon in the pasture was 3,3 times higher than in the forest, but microbial activity was similar. Carbon use rate ranged from 22,22 to 85,19% in the pasture (higher in the forest: 29,63 to 92,59%). In both areas growth correlated with incubation time, but the forest had more biodiversity. Pasture areas are favored by carbon deposition to the rhizosphere, while the variety of vegetation in the forest allows greater functional diversity in the use of carbon substrates.

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Prince, Véronique, Anne-Marie Simao-Beaunoir, and Carole Beaulieu. "Amplified ribosomal DNA restriction analysis of free-living bacteria present in the headbox of a Canadian paper machine." Canadian Journal of Microbiology 55, no. 7 (July 2009): 810–17. http://dx.doi.org/10.1139/w09-036.

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The headbox water is the main source of bacterial contamination of paper machines. Identification of these bacterial contaminants could be an asset in developing specific control methods. An amplified ribosomal DNA restriction analysis (ARDRA) was carried out to characterize the bacterial communities associated with the headbox water of a paper machine in a Canadian mill in February and July 2006. Eight bacterial genera were identified as the main colonizers present in the headbox water. The genus Meiothermus appeared to be the dominant bacterial group in the Canadian paper machine. Some variation was observed between the February and July clone libraries. Bacterial genera such as Chelatococcus and Hydrogenophilus were only detected in February or in July, respectively. Furthermore, the proportion of Tepidimonas clones in the libraries was higher in July than in February. The metabolic profile of the February and July communities, determined using Biolog EcoPlates, also suggested that temporal variation occurred within the bacterial populations that colonized the headbox of the paper machine.

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LING, YUXI, WENYING LI, TONG TONG, ZUMING LI, QIAN LI, ZHIHUI BAI, GUIJUN WANG, JIAHAO CHEN, and YUGUANG WANG. "Assessing the Microbial Communities in Four Different Daqusby Using PCR-DGGE, PLFA, and Biolog Analyses." Polish Journal of Microbiology 69, no. 1 (February 18, 2020): 27–37. http://dx.doi.org/10.33073/pjm-2020-004.

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Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

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Jurkšienė, Girmantė, Dalia Janušauskaitė, and Virgilijus Baliuckas. "Microbial Community Analysis of Native Pinus sylvestris L. and Alien Pinus mugo L. on Dune Sands as determined by Ecoplates." Forests 11, no. 11 (November 15, 2020): 1202. http://dx.doi.org/10.3390/f11111202.

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The Curonian Spit (Lithuanian: Kursiu nerija) is a 98 km long, thin, curved sand-dune spit that separates the Curonian Lagoon from the Baltic Sea coast. The Curonian Spit is home to the highest moving (drifting) sand dunes in Europe. Coniferous woods are prevalent in the Kursiu Nerija National Park (80%). These woods consist mostly of native Scots pine (Pinus sylvestris L.) and alien mountain pine (Pinus mugo L.). With the planting of non-native species, there is a need for studies evaluating the effects of alien and native plant species on soil ecosystem properties. We measured soil microbial communities from nearby pairs of native and alien pine species. Forty-two sampling sites of close-growing P. sylvestris and P. mugo were selected. To measure the soil microbial activity in these sites, we used Biolog EcoPlates. We found that the functional diversity of microorganisms that use carbon sources was significantly greater in the mature pine stands. Microbial functional diversity was also greater in the soils of native pine stands. Differences between activity and functional diversity in newly established and old stands were also identified.

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Chazarenc, Florent, Jacques Brisson, and Gérard Merlin. "Seasonal and Spatial Changes of Microorganism Communities in Constructed Wetlands: A Community Level Physiological Profiling Analysis." International Journal of Chemical Engineering 2010 (2010): 1–6. http://dx.doi.org/10.1155/2010/490240.

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In constructed wetlands, microorganisms associated with plants are assumed to play a major role. A one-year survey was conducted in five vertical flow constructed wetland systems that had been operating from 2 months to 8 years in small French villages (100–500 People Equivalent) to provide a better understanding of microbiological activity. The objective of our study was to highlight the most important factor generating variability between microorganisms communities compared to treatment performances. Results of community level physiological profiling using Biolog Ecoplates were analyzed using principal component analysis. The greatest microbial activity was observed in the oldest wetland during summer. Profiles of fed and rest bed were differentiated by the nature of the main carbon source metabolized. Whereas carbohydrates and carboxylic acids appeared to be better assimilated with fed beds, it seemed that phosphate compounds as well as amines allowed better growth in the plates inoculated with samples of rest beds. In all fed beds, the most important parameters affecting the diversity were the season and the age of the wetlands. There were only slight profile differences between surface and subsurface samples and between the first and second stage samples.

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Journal articles on the topic 'BIOLOG™ EcoPlate'

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